Multiple sequence alignment - TraesCS4A01G089600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4A01G089600 chr4A 100.000 2934 0 0 1 2934 95388437 95385504 0.000000e+00 5419.0
1 TraesCS4A01G089600 chr4A 94.157 1968 59 8 1 1939 90327923 90329863 0.000000e+00 2946.0
2 TraesCS4A01G089600 chr5A 94.528 2979 110 14 1 2931 616789255 616792228 0.000000e+00 4549.0
3 TraesCS4A01G089600 chr5A 95.414 1701 46 10 3 1674 582940411 582942108 0.000000e+00 2680.0
4 TraesCS4A01G089600 chr5A 86.379 301 13 12 1 273 129148608 129148908 1.320000e-78 303.0
5 TraesCS4A01G089600 chr6B 94.481 1975 73 24 1 1939 172269347 172267373 0.000000e+00 3011.0
6 TraesCS4A01G089600 chr6B 95.273 952 40 1 993 1939 489798396 489799347 0.000000e+00 1504.0
7 TraesCS4A01G089600 chr6B 94.147 991 52 4 603 1587 559487162 559488152 0.000000e+00 1504.0
8 TraesCS4A01G089600 chr6B 85.802 324 14 17 1 292 559486767 559487090 6.100000e-82 315.0
9 TraesCS4A01G089600 chr2D 96.928 1465 38 4 1472 2931 110056727 110055265 0.000000e+00 2449.0
10 TraesCS4A01G089600 chr2D 94.910 1002 45 4 564 1559 110057614 110056613 0.000000e+00 1563.0
11 TraesCS4A01G089600 chr2D 92.903 155 9 2 1 153 548895741 548895895 1.060000e-54 224.0
12 TraesCS4A01G089600 chr7B 93.483 1427 84 5 603 2023 209399821 209401244 0.000000e+00 2111.0
13 TraesCS4A01G089600 chr7B 88.012 1368 128 14 603 1966 286566202 286564867 0.000000e+00 1585.0
14 TraesCS4A01G089600 chr7B 95.536 560 21 3 2375 2931 332400826 332401384 0.000000e+00 893.0
15 TraesCS4A01G089600 chr7B 89.439 303 20 11 1 292 209399448 209399749 3.570000e-99 372.0
16 TraesCS4A01G089600 chr7B 95.652 184 8 0 2171 2354 332400529 332400712 2.210000e-76 296.0
17 TraesCS4A01G089600 chr7B 93.717 191 12 0 147 337 286566862 286566672 1.330000e-73 287.0
18 TraesCS4A01G089600 chr7B 85.172 290 15 3 1 262 648440775 648441064 3.730000e-69 272.0
19 TraesCS4A01G089600 chr7B 98.214 56 1 0 335 390 286566581 286566526 6.690000e-17 99.0
20 TraesCS4A01G089600 chr7B 100.000 34 0 0 357 390 15070845 15070878 2.440000e-06 63.9
21 TraesCS4A01G089600 chr3D 90.652 1380 95 17 603 1981 189780339 189781685 0.000000e+00 1803.0
22 TraesCS4A01G089600 chr3D 88.564 411 20 16 1 384 189779842 189780252 9.520000e-130 473.0
23 TraesCS4A01G089600 chr3D 95.402 87 4 0 2031 2117 415537499 415537585 3.940000e-29 139.0
24 TraesCS4A01G089600 chr7D 94.821 560 25 2 2375 2931 272825404 272824846 0.000000e+00 870.0
25 TraesCS4A01G089600 chr7D 93.571 560 30 3 2375 2931 521644058 521644614 0.000000e+00 830.0
26 TraesCS4A01G089600 chr7D 95.480 177 8 0 2175 2351 521643765 521643941 1.720000e-72 283.0
27 TraesCS4A01G089600 chr7D 93.122 189 8 3 2171 2354 272825706 272825518 3.730000e-69 272.0
28 TraesCS4A01G089600 chr5D 94.286 560 26 3 2375 2931 423848990 423848434 0.000000e+00 852.0
29 TraesCS4A01G089600 chr5D 92.737 179 13 0 2176 2354 423849282 423849104 2.900000e-65 259.0
30 TraesCS4A01G089600 chr1D 93.750 560 29 3 2375 2931 110580952 110580396 0.000000e+00 835.0
31 TraesCS4A01G089600 chr1D 87.799 418 20 17 7 395 442117801 442117386 7.410000e-126 460.0
32 TraesCS4A01G089600 chr1D 94.444 180 10 0 2175 2354 110581245 110581066 8.010000e-71 278.0
33 TraesCS4A01G089600 chr3A 93.750 560 28 4 2375 2931 726001160 726000605 0.000000e+00 833.0
34 TraesCS4A01G089600 chr3A 92.778 180 13 0 2175 2354 726001453 726001274 8.070000e-66 261.0
35 TraesCS4A01G089600 chr3A 94.253 87 5 0 2031 2117 146887049 146886963 1.830000e-27 134.0
36 TraesCS4A01G089600 chr3A 95.181 83 4 0 2031 2113 535003720 535003638 6.600000e-27 132.0
37 TraesCS4A01G089600 chr3A 86.957 92 8 4 499 587 28055696 28055606 1.860000e-17 100.0
38 TraesCS4A01G089600 chr2B 93.393 560 33 2 2375 2931 305764559 305765117 0.000000e+00 826.0
39 TraesCS4A01G089600 chr2B 94.972 179 9 0 2176 2354 305764267 305764445 6.190000e-72 281.0
40 TraesCS4A01G089600 chr3B 87.371 483 58 1 1464 1946 708716628 708717107 4.270000e-153 551.0
41 TraesCS4A01G089600 chr3B 96.296 81 3 0 2031 2111 541517975 541518055 1.830000e-27 134.0
42 TraesCS4A01G089600 chr3B 90.000 90 7 2 499 587 32732016 32731928 6.640000e-22 115.0
43 TraesCS4A01G089600 chr3B 96.364 55 0 1 2117 2169 518933907 518933853 4.030000e-14 89.8
44 TraesCS4A01G089600 chr1A 96.471 85 3 0 2033 2117 137798413 137798329 1.100000e-29 141.0
45 TraesCS4A01G089600 chr1A 96.296 54 0 1 2118 2169 137798299 137798246 1.450000e-13 87.9
46 TraesCS4A01G089600 chrUn 93.023 86 5 1 2033 2117 4345527 4345442 1.100000e-24 124.0
47 TraesCS4A01G089600 chrUn 93.023 86 5 1 2033 2117 123974652 123974567 1.100000e-24 124.0
48 TraesCS4A01G089600 chr7A 96.429 56 2 0 335 390 77196744 77196799 3.110000e-15 93.5
49 TraesCS4A01G089600 chr1B 96.364 55 0 1 2117 2169 556350723 556350669 4.030000e-14 89.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G089600 chr4A 95385504 95388437 2933 True 5419.0 5419 100.000000 1 2934 1 chr4A.!!$R1 2933
1 TraesCS4A01G089600 chr4A 90327923 90329863 1940 False 2946.0 2946 94.157000 1 1939 1 chr4A.!!$F1 1938
2 TraesCS4A01G089600 chr5A 616789255 616792228 2973 False 4549.0 4549 94.528000 1 2931 1 chr5A.!!$F3 2930
3 TraesCS4A01G089600 chr5A 582940411 582942108 1697 False 2680.0 2680 95.414000 3 1674 1 chr5A.!!$F2 1671
4 TraesCS4A01G089600 chr6B 172267373 172269347 1974 True 3011.0 3011 94.481000 1 1939 1 chr6B.!!$R1 1938
5 TraesCS4A01G089600 chr6B 489798396 489799347 951 False 1504.0 1504 95.273000 993 1939 1 chr6B.!!$F1 946
6 TraesCS4A01G089600 chr6B 559486767 559488152 1385 False 909.5 1504 89.974500 1 1587 2 chr6B.!!$F2 1586
7 TraesCS4A01G089600 chr2D 110055265 110057614 2349 True 2006.0 2449 95.919000 564 2931 2 chr2D.!!$R1 2367
8 TraesCS4A01G089600 chr7B 209399448 209401244 1796 False 1241.5 2111 91.461000 1 2023 2 chr7B.!!$F3 2022
9 TraesCS4A01G089600 chr7B 286564867 286566862 1995 True 657.0 1585 93.314333 147 1966 3 chr7B.!!$R1 1819
10 TraesCS4A01G089600 chr7B 332400529 332401384 855 False 594.5 893 95.594000 2171 2931 2 chr7B.!!$F4 760
11 TraesCS4A01G089600 chr3D 189779842 189781685 1843 False 1138.0 1803 89.608000 1 1981 2 chr3D.!!$F2 1980
12 TraesCS4A01G089600 chr7D 272824846 272825706 860 True 571.0 870 93.971500 2171 2931 2 chr7D.!!$R1 760
13 TraesCS4A01G089600 chr7D 521643765 521644614 849 False 556.5 830 94.525500 2175 2931 2 chr7D.!!$F1 756
14 TraesCS4A01G089600 chr5D 423848434 423849282 848 True 555.5 852 93.511500 2176 2931 2 chr5D.!!$R1 755
15 TraesCS4A01G089600 chr1D 110580396 110581245 849 True 556.5 835 94.097000 2175 2931 2 chr1D.!!$R2 756
16 TraesCS4A01G089600 chr3A 726000605 726001453 848 True 547.0 833 93.264000 2175 2931 2 chr3A.!!$R4 756
17 TraesCS4A01G089600 chr2B 305764267 305765117 850 False 553.5 826 94.182500 2176 2931 2 chr2B.!!$F1 755

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
824 1205 0.886490 GCGTGGAATAGGATGGCTGG 60.886 60.0 0.0 0.0 0.00 4.85 F
1313 1701 0.600782 GGGTGTTTGTGCAAGGCATG 60.601 55.0 0.0 0.0 41.91 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1892 2349 0.375106 GCCATTTCGCTCCGAAGAAG 59.625 55.000 0.22 0.0 46.43 2.85 R
2854 3414 1.202245 GCAGACACAAAAGCAACCGAA 60.202 47.619 0.00 0.0 0.00 4.30 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
327 367 3.641437 TGCTTGCTGTTATGTTTGGTC 57.359 42.857 0.00 0.00 0.00 4.02
710 1089 6.153000 TGTTGGTGTAGTTAAAAAGCCAAGAA 59.847 34.615 0.00 0.00 35.53 2.52
824 1205 0.886490 GCGTGGAATAGGATGGCTGG 60.886 60.000 0.00 0.00 0.00 4.85
885 1266 7.231317 ACAAAGATACAGATTCAGGAAAAGCAA 59.769 33.333 0.00 0.00 0.00 3.91
990 1371 1.667510 TGCTGACGCGCATCTTTGA 60.668 52.632 5.73 0.00 39.65 2.69
1257 1638 9.063615 TCCTCTCTTTTTGTTGACCTTTATAAC 57.936 33.333 0.00 0.00 0.00 1.89
1277 1663 9.737427 TTATAACGAATTTTCATTGTTGTGTGT 57.263 25.926 0.00 0.00 0.00 3.72
1307 1693 3.701542 TGATAACTTGGGTGTTTGTGCAA 59.298 39.130 0.00 0.00 0.00 4.08
1313 1701 0.600782 GGGTGTTTGTGCAAGGCATG 60.601 55.000 0.00 0.00 41.91 4.06
1846 2303 3.372822 TCAAAAGTGTTGAGAACCGTGAC 59.627 43.478 0.00 0.00 0.00 3.67
1860 2317 8.092068 TGAGAACCGTGACATCTTTCTTAATTA 58.908 33.333 0.00 0.00 0.00 1.40
1867 2324 5.095691 ACATCTTTCTTAATTATGCCGCG 57.904 39.130 0.00 0.00 0.00 6.46
1892 2349 0.880278 TGAAGAGAGTGTTGCGGTGC 60.880 55.000 0.00 0.00 0.00 5.01
1974 2431 3.263425 CCCCTTCTTCTTTGTGCTACCTA 59.737 47.826 0.00 0.00 0.00 3.08
2195 2654 6.635030 AGGTTTGTTAGTTCATCTTGGTTC 57.365 37.500 0.00 0.00 0.00 3.62
2197 2656 5.237779 GGTTTGTTAGTTCATCTTGGTTCGA 59.762 40.000 0.00 0.00 0.00 3.71
2199 2658 7.360361 GTTTGTTAGTTCATCTTGGTTCGATT 58.640 34.615 0.00 0.00 0.00 3.34
2261 2720 0.387622 CAAATCACTGCAGCCAACGG 60.388 55.000 15.27 0.00 0.00 4.44
2610 3167 8.511604 TTCATTGTAATTTTCCCTTTGCAAAA 57.488 26.923 13.84 0.00 32.50 2.44
2775 3332 1.219724 TGGTATCCTCCAGGTCCTACC 59.780 57.143 0.00 11.68 38.99 3.18
2854 3414 6.316640 TCGAAATCGTCTATTTGAGAGTCTCT 59.683 38.462 20.64 0.70 37.93 3.10
2896 3456 3.611766 CGCTACTGCTGACTTGTAGTTGA 60.612 47.826 0.00 0.00 36.84 3.18
2931 3491 4.883083 TGTCATGTACTCTCTTCCAACAC 58.117 43.478 0.00 0.00 0.00 3.32
2932 3492 4.246458 GTCATGTACTCTCTTCCAACACC 58.754 47.826 0.00 0.00 0.00 4.16
2933 3493 3.260884 TCATGTACTCTCTTCCAACACCC 59.739 47.826 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.451540 CCCTTAGAGTGTTCCCTAAGTCC 59.548 52.174 0.00 0.00 39.90 3.85
516 895 5.077564 AGAGTGAGTTGTGTGACCTACATA 58.922 41.667 0.00 0.00 42.24 2.29
710 1089 2.242043 CAAAGCTGGGTTCCATTGAGT 58.758 47.619 0.00 0.00 30.82 3.41
786 1167 2.811431 CGCTTCAGTTGACCAACCATTA 59.189 45.455 9.07 0.00 42.06 1.90
824 1205 8.196771 TGTGGCCATATCTTTCATGAAATAAAC 58.803 33.333 20.76 9.78 0.00 2.01
885 1266 5.763204 TCGGTATTGAGCTTTCAAGTCTTTT 59.237 36.000 0.00 0.00 32.69 2.27
937 1318 4.711846 TGTATGATAGTTCCAGCTGACACT 59.288 41.667 17.39 18.05 0.00 3.55
990 1371 7.865706 AGAACTTACAGTCATCAAGTTTTGT 57.134 32.000 1.54 0.00 41.36 2.83
1257 1638 5.280945 AGGACACACAACAATGAAAATTCG 58.719 37.500 0.00 0.00 0.00 3.34
1277 1663 7.507616 ACAAACACCCAAGTTATCATTAAAGGA 59.492 33.333 0.00 0.00 0.00 3.36
1307 1693 2.840651 AGTTACCTTCTGCTACATGCCT 59.159 45.455 0.00 0.00 42.00 4.75
1313 1701 7.041372 TGTGAAATTGAAGTTACCTTCTGCTAC 60.041 37.037 1.45 0.00 46.07 3.58
1507 1895 0.543277 CACTTGGGGCAGCATCTCTA 59.457 55.000 0.00 0.00 0.00 2.43
1846 2303 4.213270 TCCGCGGCATAATTAAGAAAGATG 59.787 41.667 23.51 0.00 0.00 2.90
1860 2317 0.531532 CTCTTCATCTTCCGCGGCAT 60.532 55.000 23.51 9.45 0.00 4.40
1867 2324 2.670414 CGCAACACTCTCTTCATCTTCC 59.330 50.000 0.00 0.00 0.00 3.46
1892 2349 0.375106 GCCATTTCGCTCCGAAGAAG 59.625 55.000 0.22 0.00 46.43 2.85
1974 2431 7.201714 GCATGCTCTAAATCTTGAGTTCTTGAT 60.202 37.037 11.37 0.00 33.22 2.57
2261 2720 2.292103 TTGCCAAACAAGTTCAGTGC 57.708 45.000 0.00 0.00 33.24 4.40
2472 3029 5.640189 AAAGCAAGAAGAATCTGATGTGG 57.360 39.130 0.00 0.00 35.59 4.17
2610 3167 2.883026 ACTTCAGAGGCTGTAGACTGT 58.117 47.619 7.86 0.00 33.94 3.55
2700 3257 6.014755 TCCCTTGCATAAACAACAATGATCAA 60.015 34.615 0.00 0.00 0.00 2.57
2775 3332 3.319137 TCCACTTCTCAATCTGGTTCG 57.681 47.619 0.00 0.00 0.00 3.95
2854 3414 1.202245 GCAGACACAAAAGCAACCGAA 60.202 47.619 0.00 0.00 0.00 4.30
2896 3456 7.341805 AGAGTACATGACAGGAGCATAAATTT 58.658 34.615 0.00 0.00 0.00 1.82


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.